From this you can see that negotiation and the original quality are important, but also important is the agent effective standing.

With agent effective standing, you start with the highest of faction, corp, and agent standings and apply the connections skill bonus to that (or diplomacy, but then you are likely a ways off from the max standing gain). So connections is also important in getting the maximum rewards. Furthermore, agent standing goes up much faster than corp standing - so sticking with one agent may be more rewarding than moving up to a higher natural quality agent with poorer effective standing and thus poorer effective quality.

Loyalty points are often an important part in mission rewards. These are worth approximately 1k isk for each loyalty point when used to buy faction equipment. High end missions can give several thousand loyalty points in addition to direct isk rewards. Training the appropriate division connections skill for a particular agent can result in significant gains for high level missions.

Lastly, there is the security status of the system the agent is in. The lower the system security status, the higher the rewards. Missions in 0.0 are much more rewarding than those in high sec. The difference can even be seen between an agent in a 1.0 system and an agent in an 0.5 system.

The Negotiation skill gives you an additional 5% pay per mission. In addition to that the connection skills (bureaucratic connections, criminal connections, etc) give you an additional 5% loyalty point gain when working for an appropriate agent.

Another good source of isk in missions is salvaging wrecks and reprocessing dropped loot. Reprocessing will likely be weakened with Tyrannis, coming in 10 days, but salvaging will still get you more loot to sell.

There are a couple good tutorials found on the web. The main skill you need for this is Salvaging which doesn't have too many prerequisites.